Unless I'm reading this wrong, the package version in "database" is different from the one I have installed, so of course its going to fail. I've checked, and my package versions are the newest ones. I also noticed that a lot of thigns got updated last night with the nightly cpanel/redhat package updates. Also, the only thing i'm having problems with is the incorrect MD5 hashes. Nothing else is detected, and nothing is suspicious at all with chkrootkit. I've done a brief analysis of my system, and it doesn't appear to be doing anything that it's not supposed to. What steps can be taken to further verify whether this is a problem or not?
EDIT: Also, I updated to cpanel PRO yesterday, and today is the first day this issue has surfaced.
Thank you.